Biological Assembly 1  

 3D View: Structure | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 70.27 kDa 
• Atom Count: 4555 
• Modelled Residue Count: 501 
• Deposited Residue Count: 624 
• Unique protein chains: 3

1O5D

Dissecting and Designing Inhibitor Selectivity Determinants at the S1 site Using an Artificial Ala190 Protease (Ala190 uPA)

• DOI: 10.2210/pdb1O5D/pdb

• Classification: BLOOD CLOTTING, hydrolase
• Organism(s): Homo sapiens
• Expression System: Homo sapiens, Escherichia coli
• Mutation(s): No 


• Deposited: 2003-09-09 Released: 2004-09-21 
• Deposition Author(s): Katz, B.A., Luong, C., Ho, J.D., Somoza, J.R., Gjerstad, E., Tang, J., Williams, S.R., Verner, E., Mackman, R.L., Young, W.B., Sprengeler, P.A., Chan, H., Mortara, K., Janc, J.W., McGrath, M.E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 0.262 
• R-Value Work: 0.226 
• R-Value Observed: 0.228 

Literature

Dissecting and designing inhibitor selectivity determinants at the S1 site using an artificial Ala190 protease (Ala190 uPA).

Katz, B.A., Luong, C., Ho, J.D., Somoza, J.R., Gjerstad, E., Tang, J., Williams, S.R., Verner, E., Mackman, R.L., Young, W.B., Sprengeler, P.A., Chan, H., Mortara, K., Janc, J.W., McGrath, M.E.

(2004) J Mol Biol 344: 527-547

• PubMed: 15522303 
• DOI: 10.1016/j.jmb.2004.09.032
• Primary Citation of Related Structures:  
  1O5A, 1O5B, 1O5C, 1O5D, 1O5E, 1O5F, 1O5G


• PubMed Abstract: 
  

A site-directed mutant of the serine protease urokinase-type plasminogen activator (uPA), was produced to assess the contribution of the Ser190 side-chain to the affinity and selectivity of lead uPA inhibitors in the absence of other differences present in comparisons of natural proteases. Crystallography and enzymology involving WT and Ala190 uPA were used to calculate free energy binding contributions of hydrogen bonds involving the Ser190 hydroxyl group (O(gamma)(Ser190)) responsible for the remarkable selectivity of 6-halo-5-amidinoindole and 6-halo-5-amidinobenzimidazole inhibitors toward uPA and against natural Ala190 protease anti-targets. Crystal structures of uPA complexes of novel, active site-directed arylguanidine and 2-aminobenzimidazole inhibitors of WT uPA, together with associated K(i) values for WT and Ala190 uPA, also indicate a significant role of Ser190 in the binding of these classes of uPA inhibitors. Structures and associated K(i) values for a lead inhibitor (CA-11) bound to uPA and to five other proteases, as well as for other leads bound to multiple proteases, help reveal the features responsible for the potency (K(i)=11nM) and selectivity of the remarkably small inhibitor, CA-11. The 6-fluoro-5-amidinobenzimidzole, CA-11, is more than 1000-fold selective against natural Ala190 protease anti-targets, and more than 100-fold selective against other Ser190 anti-targets.

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Organizational Affiliation: 

Celera, 180 Kimball Way, South San Francisco, CA 94080, USA. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Coagulation factor VII	A [auth L]	152	Homo sapiens	Mutation(s): 0  Gene Names: F7 EC: 3.4.21.21
UniProt & NIH Common Fund Data Resources
Find proteins for P08709 (Homo sapiens) Explore P08709  Go to UniProtKB:  P08709
PHAROS:  P08709 GTEx:  ENSG00000057593

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Coagulation factor VII	B [auth H]	254	Homo sapiens	Mutation(s): 0  Gene Names: F7 EC: 3.4.21.21
UniProt & NIH Common Fund Data Resources
Find proteins for P08709 (Homo sapiens) Explore P08709  Go to UniProtKB:  P08709
PHAROS:  P08709 GTEx:  ENSG00000057593

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Tissue factor	C [auth T]	218	Homo sapiens	Mutation(s): 0  Gene Names: F3
UniProt & NIH Common Fund Data Resources
Find proteins for P13726 (Homo sapiens) Explore P13726  Go to UniProtKB:  P13726
PHAROS:  P13726 GTEx:  ENSG00000117525

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CR9 (Subject of Investigation/LOI)	D [auth H]	2-{5-[AMINO(IMINIO)METHYL]-6-FLUORO-1H-BENZIMIDAZOL-2-YL}-6-[(2-METHYLCYCLOHEXYL)OXY]BENZENOLATE C21 H23 F N4 O2 CMCDWLMEDRBWIR-GTNSWQLSSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 0.262 
• R-Value Work: 0.226 
• R-Value Observed: 0.228 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.54	α = 90
b = 69.03	β = 89.99
c = 79.12	γ = 90

Software Package:

Software Name	Purpose
ALS Berkeley beamline 5.0.2	data collection
DENZO	data reduction
X-PLOR	refinement
SCALEPACK	data scaling
Quanta	model building

Structure Validation

Ligand Structure Quality Assessment  

Entry History 

Deposition Data

• Deposited Date: 2003-09-09 
• Released Date: 2004-09-21 
Deposition Author(s): Katz, B.A., Luong, C., Ho, J.D., Somoza, J.R., Gjerstad, E., Tang, J., Williams, S.R., Verner, E., Mackman, R.L., Young, W.B., Sprengeler, P.A., Chan, H., Mortara, K., Janc, J.W., McGrath, M.E.

Revision History  

• Version 1.0: 2004-09-21
  Type: Initial release
  
• Version 1.1: 2008-04-26
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-04
  Changes: Refinement description